This work presents a new algorithm, called Heterogeneous Dynamic Pipeline Mapping, that allows for dynamically improving the performance of pipeline applications running on heterogeneous systems. It is aimed at balancing the application load by determining the best replication (of slow stages) and gathering (of fast stages) combination taking into account processors computation and communication capacities. In addition, the algorithm has been designed with the requirement of keeping complexity low to allow its usage in a dynamic tuning tool. For this reason, it uses an analytical performance model of pipeline applications that addresses hardware heterogeneity and which depends on parameters that can be known in advance or This work has been partially supported by Ministerio de Economía y Competitividad MINECO-Spain under contract TIN2014-53234-C2-1-R and Generalitat de Catalunya GenCat-DIUiE (GRR) 2014-SGR-576.